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1. USAGE

To run the Software Package from the command line using default parameters, Run the run_predict_binding.py script as:

./run_predict_binding.py XXXX.pdb

2. INPUT

The three dimensional coordinates of the atomic positions of the protein complex should be given in a PDB format. Place the PDB files in the 'input' directory of the package.

3. OUTPUT

After a successful run of the program, the corresponding output files are generated in the 'output' directory. For each complex, two text files will be generated -

1. XXXX_scores.out - Contains the prediction and other metrics like z-score
2. XXXX_respairs.out - Contains the residue pairs comprising the interface

In case the Alanine Scanning flag is provided, an additional file will be generated, 3. XXXX_alascan.out - Contains the residues which upon mutation might destabilize the interaction

4. EXAMPLES

Examples for the input and output files are provided in the 'examples' directory

5. ADDITIONAL PARAMETERS

Optional flags that can be turned on - USAGE:

./run_predict_binding.py XXXX.pdb -d 8.0 -t mm

1. Distance threshold for interaction definition: -d, --cutoff, choices = {4.0, 6.0, 8.0} NOTE: Default value = 4.0

2. Types of interacting atoms between residues: -t, --intertype, choices = {'all', 'mm', 'ms', 'ss'} NOTE: Default value = ss all - Interactions between all atoms mm - Interactions between main chain atoms ms - Interactions between main chain atoms and side chain atoms ss - Interactions between side chain atoms

3. To specify your own 20x20 matrix for residue-pair scores: -cp, --custom_pot, file NOTE: The custom potential should be in the format of a .csv file with the residue_pair in first column and the corresponding score in the second column. Example file provided in the 'examples' directory (custom_pot.csv)

4. To perform Alanine Scanning with the default potential: -alscn, --alascan, choices = {'0', 1', '2', '3'} NOTE: Default value = '0' 0 - Do not perform Alanine Scanning 1 - Mutate all the residues on the interface to Alanine 2 - Mutate all the residues on the interface to every other residue 3 - Mutate a given list of residues to every other residue (residues to be provided in a separate file)

   *NOTE: In case mode '3' is selected, a separate file containing the residues to be mutated should be provided in the 'input' directory. An example file is given in the 'examples' directory (4pza_alscan_input.txt).

5. In case of multimers, specify particular interfaces, -p1, -p2, --protein_1, --protein_2

6. To specify a name for the output files, -o, --outfile

This help can be accessed on the command line using: ./run_predict_binding.py -h or ./run_predict_binding.py --help

6. SOURCE CODE

All the scripts for the package can be found in the 'scripts' directory.

7. LICENSE

Please refer to COPYING.txt for the full license or COPYING_LESSER.txt for a condensed version.